├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── .lintr ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── 1_1_model.R ├── 1_2_model_tune.R ├── 1_3_model_method.R ├── 2_1_nomogram.R ├── 2_2_convert_model.R ├── 2_3_survial_curves.R ├── 2_4_nomogram_method.R ├── 3_1_validate.R ├── 3_2_validate_utils.R ├── 3_3_validate_method.R ├── 3_4_validate_external.R ├── 3_5_validate_external_utils.R ├── 3_6_validate_external_method.R ├── 4_1_calibrate.R ├── 4_2_calibrate_utils.R ├── 4_3_calibrate_method.R ├── 4_4_calibrate_external.R ├── 4_5_calibrate_external_utils.R ├── 4_6_calibrate_external_method.R ├── 4_7_kmplot.R ├── 4_8_logrank_test.R ├── 5_1_compare_by_validate.R ├── 5_2_compare_by_validate_method.R ├── 5_3_compare_by_calibrate.R ├── 5_4_compare_by_calibrate_method.R ├── datalist.R ├── hdnom.R ├── palettes.R ├── rms_nomogram.R ├── rms_nomogram_method.R ├── rms_nomogram_misc.R ├── survAUC_ChamDiao.R ├── survAUC_Song_Zhou.R ├── survAUC_Uno.R ├── survAUC_utils.R └── theme_hdnom.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data-raw └── smart.R ├── data ├── smart.rda └── smarto.rda ├── hdnom.Rproj ├── inst ├── AUTHORS ├── CITATION └── logo │ └── logo.R ├── man ├── as_nomogram.Rd ├── calibrate.Rd ├── calibrate_external.Rd ├── calibrate_external_surv_prob_true.Rd ├── calibrate_surv_prob_true.Rd ├── compare_by_calibrate.Rd ├── compare_by_validate.Rd ├── figures │ ├── README-kmplot-1.png │ ├── README-model-comparison-1.png │ ├── README-model-validation-calibration-1.png │ ├── README-nomogram-1.png │ └── logo.png ├── fit_aenet.Rd ├── fit_alasso.Rd ├── fit_enet.Rd ├── fit_flasso.Rd ├── fit_lasso.Rd ├── fit_mcp.Rd ├── fit_mnet.Rd ├── fit_scad.Rd ├── fit_snet.Rd ├── glmnet_basesurv.Rd ├── glmnet_calibrate_external_surv_prob_pred.Rd ├── glmnet_calibrate_surv_prob_pred.Rd ├── glmnet_survcurve.Rd ├── glmnet_tune_alpha.Rd ├── glmnet_validate_external_tauc.Rd ├── glmnet_validate_tauc.Rd ├── hdnom-package.Rd ├── infer_variable_type.Rd ├── kmplot.Rd ├── kmplot_raw.Rd ├── logrank_test.Rd ├── ncvreg_basesurv.Rd ├── ncvreg_calibrate_external_surv_prob_pred.Rd ├── ncvreg_calibrate_surv_prob_pred.Rd ├── ncvreg_survcurve.Rd ├── ncvreg_tune_gamma.Rd ├── ncvreg_tune_gamma_alpha.Rd ├── ncvreg_validate_external_tauc.Rd ├── ncvreg_validate_tauc.Rd ├── palette_aaas.Rd ├── palette_jco.Rd ├── palette_lancet.Rd ├── palette_npg.Rd ├── penalized_basesurv.Rd ├── penalized_calibrate_external_surv_prob_pred.Rd ├── penalized_calibrate_surv_prob_pred.Rd ├── penalized_survcurve.Rd ├── penalized_tune_lambda.Rd ├── penalized_validate_external_tauc.Rd ├── penalized_validate_tauc.Rd ├── plot.hdnom.calibrate.Rd ├── plot.hdnom.calibrate.external.Rd ├── plot.hdnom.compare.calibrate.Rd ├── plot.hdnom.compare.validate.Rd ├── plot.hdnom.nomogram.Rd ├── plot.hdnom.validate.Rd ├── plot.hdnom.validate.external.Rd ├── predict.hdnom.model.Rd ├── print.hdnom.calibrate.Rd ├── print.hdnom.calibrate.external.Rd ├── print.hdnom.compare.calibrate.Rd ├── print.hdnom.compare.validate.Rd ├── print.hdnom.model.Rd ├── print.hdnom.nomogram.Rd ├── print.hdnom.validate.Rd ├── print.hdnom.validate.external.Rd ├── smart.Rd ├── smarto.Rd ├── summary.hdnom.calibrate.Rd ├── summary.hdnom.calibrate.external.Rd ├── summary.hdnom.compare.calibrate.Rd ├── summary.hdnom.compare.validate.Rd ├── summary.hdnom.validate.Rd ├── summary.hdnom.validate.external.Rd ├── theme_hdnom.Rd ├── validate.Rd └── validate_external.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── src ├── Makevars ├── hdnom-init.c ├── survAUC_Cham_Diao.c ├── survAUC_Cham_Diao.h ├── survAUC_SongZhou.c ├── survAUC_SongZhou.h ├── survAUC_UNO.c 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